[gmx-developers] Segmentation fault switching from group to verlet cutoff shceme

Mark Abraham mark.j.abraham at gmail.com
Fri Mar 15 22:48:55 CET 2013

On Fri, Mar 15, 2013 at 8:58 PM, Bu Wang <bw2 at alfred.edu> wrote:

> Hello,
> We encountered a problem with the verlet cutoff scheme in GROMACS 4.6.1. A
> simulation that works fine with the group scheme will crash with
> "Segmentation fault: 11" error using the verlet method. GDB shows that it
> happens in pme.c: 415 idxptr[ZZ] = pme->nnz[tiz], but we are not sure how
> to proceed from here.

Sounds suspicious. Please open an issue at redmine.gromacs.org with a
description of your simulation, and preferably .mdp and .tpr files.

It is possible that our simulation is blowing up, as we can see the
> non-bonded energy becomes absurd in the very first step after switching to
> verlet scheme. However, we don't see how it is possible that the same
> simulation would work with the group scheme. The group scheme gives correct
> energies, and can run to the end without any problem.

That does make it sound like it might be a bug. Can you take your group
scheme .tpr and use mdrun -testverlet successfully?

To further diagnose the problem, we are wondering how we can let GROMACS
> output the neighbor list. We would also greatly appreciate any suggestion
> to resolve the problem.

The construction of the neighbour lists is different between group and
Verlet kernels, so there is not much to gain from inspecting them. Knowing
the combination of algorithms in use is of more interest (so .mdp and any
mdrun command line options).

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